A Simple, Pragmatic Explanation

For A to be "not different" from B, or equivalent to B A must equal B. A is represented by the first comparison, of atheists to theists. B is represented by the second comparison, of whites to blacks. "Atheists" does not equal "whites" by definition, and "theists" does not equal "blacks" by definition, thus the two comparisons are not copies of each other, i.e. the same, but merely related.

There is a difference between belief and ethnicity

Being white or black is not a choice, a belief is a choice. There can be no logic involved in a skin color being better than another. Whether or not the logic is correct, it can be used in the first statement. You could ask if one was worse to say, but not if they are the same.

Yes it is different

It is exactly like claiming that mentally challenged people are less intelligent than people with high IQ scores or stating that Neo nazis are foolish. It might be crass and show a great deal of social inability when talking to those people, but it is true, unlike stating that different ethnic groups are evil or dangerous.

They are baseless claims:

Any form of baseless claim argued on arbitrary terms is a fallacy so it is here. Your intelligence or knowledge base have nothing to do with your beliefs relative to deities. Generally speaking it's a commonly accepted error so it's widespread but it makes absolutely not one lick of sense.

Yes it is different

It is exactly like claiming that mentally challenged people are less intelligent than people with high IQ scores or stating that Neo nazis are foolish. It might be crass and show a great deal of social inability when talking to those people, but it is true, unlike stating that different ethnic groups are evil or dangerous.

I think not.

Any way you look at it, you have one group claiming to be superior to the other. I don't see any difference at all. Some might say that being black is not a choice and religion is, but I would have to disagree. Deeply held beliefs are integral to who a person is. I could no more change my faith than I could change my skin color. In either case, you have some idiot claiming to be superior to someone else. And that's wrong, no matter how you slice it.

Of course it not the same. On the specific subject of religion an atheist would be more intelligent than a theist. This is because to believe in god and all the dogma and bizarre stories that go with it all, to shape your life around that isn't the most intelligent thing to do. But that's not to say a religious person couldn't beat an atheist at chess for example.